Binding of 2-Aryl-4-(piperidin-1-yl)butanamines and 1,3,4-Trisubstituted Pyrrolidines to Human CCR5:  A Molecular Modeling-Guided Mutagenesis Study of the Binding Pocket

Abstract

The results of investigations in these laboratories of 2-aryl-4-(piperidin-1-yl)butanamines and 1,3,4-trisubstituted pyrrolidines as human CCR5 antagonists have recently been disclosed. To facilitate further development of these antagonists, we have developed a pharmacophore model based on the structure-activity relationships (SAR) and a human CCR5 receptor docking model using the crystal structure of rhodopsin as a template [Palczewski, K., et al. (2000) Science 289, 739-745]. Guided by the receptor docking model, we have mapped the compounds' site of interaction with CCR5 using site-directed mutagenesis experiments. Our results are consistent with a binding site for the two series that is located within a cavity near the extracellular surface formed by transmembrane helices 2, 3, 6, and 7. This site is overlapping yet distinct from that reported for another antiviral agent which binds to CCR5 [Dragic, T., et al. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 5639-5644].

Molecular Interaction of a Potent Nonpeptide Agonist with the Chemokine Receptor CCR8

“…The left side of LMD-009 is suggested to be in close proximity to and dependent upon TyrIII:08 in the major binding pocket as described for almost all characterized CC-chemokine receptor antagonists (Berkhout et al, 2003;Castonguay et al, 2003;de Mendonça et al, 2005;Maeda et al, 2006;Vaidehi et al, 2006) and position III:08-in the form of an Asp-is also a key-interaction point for the monoamines . The orientation of LMD-009 was mainly provided by studying the four analogs, LMD-584, LMD-902, LMD-268, and LMD-174, with variation in the left side compared with LMD-009, because they all reacted very differently from LMD-009 to mutations in the major binding pocket.…”

“…Nonpeptide antagonists against CC-chemokine receptors usually share a common pharmacophore with a rather centrally located, positively charged amine Seibert et al, 2006). This amine has been shown to interact with a highly conserved Glu in the extracellular end of TM-VII (in position VII:06), whereas the flanking groups have been shown to interact with conserved aromatic residues, as well as other residues specific for each chemokine receptor (Mirzadegan et al, 2000;Castonguay et al, 2003;Tsamis et al, 2003;de Mendonça et al, 2005;Maeda et al, 2006;Seibert et al, 2006). Thus, all CC-chemokine receptor nonpeptide antagonists with characterized binding modes interact with GluVII:06 [except for the recently characterized binding pocket of BX471 in CCR1 (Vaidehi et al, 2006)] in addition to aromatic residues in the major binding pocket (composed of TM-III, TM-IV, TM-V, TM-VI, and TM-VII) and in the minor binding pocket (composed of TM-I, TM-II, TM-III, and TM-VII) ( Fig.…”

“…Thus, all CC-chemokine receptor nonpeptide antagonists with characterized binding modes interact with GluVII:06 [except for the recently characterized binding pocket of BX471 in CCR1 (Vaidehi et al, 2006)] in addition to aromatic residues in the major binding pocket (composed of TM-III, TM-IV, TM-V, TM-VI, and TM-VII) and in the minor binding pocket (composed of TM-I, TM-II, TM-III, and TM-VII) ( Fig. 1) (Mirzadegan et al, 2000;Castonguay et al, 2003;Tsamis et al, 2003;de Mendonça et al, 2005;Maeda et al, 2006;Seibert et al, 2006). Like most chemokine receptor nonpeptide ligands, LMD-009 contains a positively charged amine (the piperidine-ring of the spiro system).…”

“…Because of the similarities in the pharmacophore of LMD-009 to many CC-chemokine receptor antagonists (Mirzadegan et al, 2000;Castonguay et al, 2003;Tsamis et al, 2003;de Mendonça et al, 2005;Maeda et al, 2006;Seibert et al, 2006;Seibert et al, 2006) as described above, it was tempting to believe that LMD-009 would in fact act as an antagonist for other CC-chemokine (or maybe even CXC-chemokine) receptors. We therefore repeated the activity screen of LMD-009, this time as antagonist.…”

Chemokine Receptors as Therapeutic Targets in HIV Infection

“…In the absence of a high-resolution structure of a gp120-coreceptor complex, biochemical studies of CCR5 have revealed the importance of its Nterminus (Nt) and second extracellular loop (ECL2) in binding gp120 and mediating viral entry (reviewed in [34]). Small molecule CCR5 inhibitors, on the other hand, are believed to bind within a cavity between the transmembrane (TM) helices on the extracellular surface of the coreceptor, as suggested by site-directed mutagenesis experiments and molecular modeling of CCR5 on the basis of the available crystal structure of bovine rhodopsin that is characterized by a similar TM topology [100,101]. More specifically, the binding "pocket" of such molecules as TAK-779, AD101, and SCH-C is thought to be located between TM helices 1-3, and 7; other TM helices, particularly helix 6, contribute to some compound-specific variations [102,103].…”